In previous versions of Internet Information Services (IIS) configurations were stored in the registry. Part of IIS 6.0's rebuilding was changing where the configuration is stored, which is now a file named MetaBase.xml in your \WINDOWS\system32\inetsrv directory. Sure, you can copy that file (and possibly MBSchema.bin.00000000h) to a separate directory, but a smarter way to do this is to use IIS 6.0's built-in back-up mechanism. There are 2 ways to do this, but I'll only be showing you the graphical one at the moment.
Method:
(Backing up Internet Information Service 6.0)
Load IIS from the Administrative tools in the Control Panel by clicking Start -> Administrative Tools -> IIS Manager (or loading the Control Panel, entering the Administrative Tools folder, and double clicking IIS Manager).
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Click Create Backup
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Your backup is stored in C:\WINDOWS\system32\inetsrv\MetaBack under the name you gave it. Actually, it will be 2 files. In the example I gave above 2 files were created:
visualwin backup.MD0
visualwin backup.SC0
I recommend the copying of these files to another folder, just in case.